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                <h1 id="功能" class="article-heading"><a href="#功能" class="headerlink" title="功能"></a>功能<a class="article-anchor" href="#功能" aria-hidden="true"></a></h1><blockquote>
<p>submit pod as workflow to argo/kubernetes</p>
</blockquote>
<ul>
<li>投递单个job到argo/k8s<h1 id="参数" class="article-heading"><a href="#参数" class="headerlink" title="参数"></a>参数<a class="article-anchor" href="#参数" aria-hidden="true"></a></h1><figure class="highlight plain"><table><tr><td class="code"><pre><span class="line">Arguments:</span><br><span class="line"></span><br><span class="line">  -p  --podConfig    pod config:</span><br><span class="line">  -t  --submit_type  Operation mode for submitting job</span><br><span class="line">		       argo  submit job as workflow type to argo.</span><br><span class="line">		       pod   submit job as pod type to kubectl.</span><br><span class="line">		       job   submit job as job type to kubectl</span><br><span class="line">		       . Default: argo</span><br><span class="line">  -h  --help         Print help information</span><br><span class="line"></span><br></pre></td></tr></table></figure>
<h2 id="p" class="article-heading"><a href="#p" class="headerlink" title="-p"></a><code>-p</code><a class="article-anchor" href="#p" aria-hidden="true"></a></h2>此项为投递单个pod的config到argo/k8s，config内各项的释义详见<a target="_blank" rel="noopener external nofollow noreferrer" href="https://gitlab.com/seqyuan/gomonitor/wikis/agsTask" title="podConfig">config</a>，示例<code>bcl2fq.ini</code>文件内容如下：<figure class="highlight shell"><table><tr><td class="code"><pre><span class="line">[templetes]</span><br><span class="line">pod_name = bcl2fq-all</span><br><span class="line">module = qc</span><br><span class="line">template = bcl2fq</span><br><span class="line">imagePullSecrets = registry-read-only-key-yw</span><br><span class="line"></span><br><span class="line">[Tolerations.network]</span><br><span class="line">Operator = Equal</span><br><span class="line">Value = internet</span><br><span class="line">Effect = NoSchedule</span><br><span class="line"></span><br><span class="line">[NodeSelector]</span><br><span class="line">env = idc_physical</span><br><span class="line"></span><br><span class="line">[requests]</span><br><span class="line">memory = 1</span><br><span class="line">cpu = 1</span><br><span class="line"></span><br><span class="line">[limits]</span><br><span class="line">memory = 1</span><br><span class="line">cpu = 1</span><br><span class="line"></span><br><span class="line">[container]</span><br><span class="line">image = registry-vpc.cn-hangzhou.aliyuncs.com/annoroad/annogene-base:v0.1</span><br><span class="line">args = /home/zanyuan/bin/example/submit_test/bcl2fq.sh</span><br><span class="line">lines = </span><br><span class="line">[volumeMounts]</span><br><span class="line">home = /cluster_home|store|/home</span><br></pre></td></tr></table></figure>
<h2 id="t" class="article-heading"><a href="#t" class="headerlink" title="-t"></a><code>-t</code><a class="article-anchor" href="#t" aria-hidden="true"></a></h2><code>-t</code>有3种可选：argo、job、pod，默认为argo</li>
<li> argo：会以workflow的形式投递单个任务到argo，适合用ags get agsID –metrics查看任务消耗的memory/cpu</li>
<li> pod：一般用于建立持久的长时运行服务，例如gitlab-runner service, Mysql </li>
<li> job：多用于执行一次性任务、批处理工作等，执行完成后便会停止（status.phase变为Succeeded）</li>
</ul>
<h1 id="example" class="article-heading"><a href="#example" class="headerlink" title="example"></a>example<a class="article-anchor" href="#example" aria-hidden="true"></a></h1><p>如果我们要投递<code>bcl2fq.sh</code>这个脚本，脚本的内容如下，需要前述的bcl2fq.ini配置信息：</p>
<figure class="highlight shell"><table><tr><td class="code"><pre><span class="line">echo 32</span><br><span class="line">sleep 6s</span><br><span class="line">echo 34</span><br><span class="line">sleep 7s</span><br><span class="line">echo 45</span><br><span class="line">sleep 5s</span><br></pre></td></tr></table></figure>
<p>you can invoke this from the command line as follows:</p>
<blockquote>
<p> 执行此命令<code>gomonitor submit -p bcl2fq.ini</code>会返回agsID</p>
</blockquote>
<p>bcl2fq-bcl2fq-all-tt7xn</p>
<blockquote>
<p>使用ags get agsID命令查看任务运行情况；如果指定了-t 参数为pod，可以用<code>kubectl get pod podID</code>命令查询任务的状态；如果指定了-t 参数为job，可以用<code>kubectl get job podID</code>命令查询任务的状态</p>
</blockquote>
<p><code>ags get bcl2fq-bcl2fq-all-tt7xn</code></p>
<figure class="highlight plain"><table><tr><td class="code"><pre><span class="line">Name:                bcl2fq-bcl2fq-all-tt7xn</span><br><span class="line">Namespace:           zanyuan</span><br><span class="line">ServiceAccount:      default</span><br><span class="line">Status:              Succeeded</span><br><span class="line">Created:             Thu Jul 11 17:25:30 +0800 (45 seconds ago)</span><br><span class="line">Started:             Thu Jul 11 17:25:30 +0800 (45 seconds ago)</span><br><span class="line">Finished:            Thu Jul 11 17:25:52 +0800 (23 seconds ago)</span><br><span class="line">Duration:            22 seconds</span><br><span class="line"></span><br><span class="line">STEP                        PODNAME                  DURATION  MESSAGE</span><br><span class="line"> ✔ bcl2fq-bcl2fq-all-tt7xn  bcl2fq-bcl2fq-all-tt7xn  20s            </span><br></pre></td></tr></table></figure>
<p><strong>标准输出流</strong>和<strong>标准错误</strong>流会类似于qsub-sge系统的job分别输出到<code>job_sh.o.+podID</code>及<code>job_sh.e.+podID</code></p>
<p>例如示例以上的标准输出流和标准错误流会分别定向到：</p>
<ul>
<li>./bcl2fq.sh.o.bcl2fq-bcl2fq-all-tt7xn</li>
<li>./bcl2fq.sh.e.bcl2fq-bcl2fq-all-tt7xn</li>
</ul>
<h2 id="高级的使用示例，使用containersection里的linesoption" class="article-heading"><a href="#高级的使用示例，使用containersection里的linesoption" class="headerlink" title="高级的使用示例，使用containersection里的linesoption"></a>高级的使用示例，使用<code>container</code>section里的<code>lines</code>option<a class="article-anchor" href="#高级的使用示例，使用containersection里的linesoption" aria-hidden="true"></a></h2><p>例如<code>bcl2fq.sh</code>这个脚本里的内容如下：</p>
<figure class="highlight shell"><table><tr><td class="code"><pre><span class="line">echo 32</span><br><span class="line">sleep 6s</span><br><span class="line">echo 34</span><br><span class="line">sleep 7s</span><br><span class="line">echo 45</span><br><span class="line">sleep 5s</span><br></pre></td></tr></table></figure>
<p>如果我们想让其每2行作为一个单位，并行的去执行，任务config <code>bcl2fq.ini</code>可以按如下配置：</p>
<figure class="highlight plain"><table><tr><td class="code"><pre><span class="line">[templetes]</span><br><span class="line">pod_name &#x3D; bcl2fq-all</span><br><span class="line">module &#x3D; qc</span><br><span class="line">template &#x3D; bcl2fq</span><br><span class="line">imagePullSecrets &#x3D; registry-read-only-key-yw</span><br><span class="line"></span><br><span class="line">[NodeSelector]</span><br><span class="line">env &#x3D; idc_physical</span><br><span class="line"></span><br><span class="line">[requests]</span><br><span class="line">memory &#x3D; 1</span><br><span class="line">cpu &#x3D; 1</span><br><span class="line"></span><br><span class="line">[limits]</span><br><span class="line">memory &#x3D; 1</span><br><span class="line">cpu &#x3D; 1</span><br><span class="line"></span><br><span class="line">[container]</span><br><span class="line">image &#x3D; registry-vpc.cn-hangzhou.aliyuncs.com&#x2F;annoroad&#x2F;annogene-base:v0.1</span><br><span class="line">args &#x3D; &#x2F;home&#x2F;zanyuan&#x2F;bin&#x2F;example&#x2F;submit_test&#x2F;bcl2fq.sh</span><br><span class="line">lines &#x3D; 2</span><br><span class="line">[volumeMounts]</span><br><span class="line">home &#x3D; &#x2F;cluster_home|store|&#x2F;home</span><br></pre></td></tr></table></figure>
<p>与前面<code>bcl2fq.ini</code>配置的唯一区别是设置了<code>lines = 2</code>，表示的意思是<code>bcl2fq.sh</code>这个脚本中每2行一个单位并行的去执行；如果想bcl2fq.sh作为一个整体串行的去执行，lines的value设置为空就可以。</p>
<blockquote>
<p>我们可以看下并行执行的效果<code>gomonitor submit -p bcl2fq.ini</code>，得到以下agsID</p>
</blockquote>
<p>bcl2fq-bcl2fq-all-8xz6h</p>
<p>查看任务运行情况，执行此命令<code>ags get bcl2fq-bcl2fq-all-8xz6h</code></p>
<figure class="highlight plain"><table><tr><td class="code"><pre><span class="line">STEP                        PODNAME                             DURATION  MESSAGE</span><br><span class="line"> ● bcl2fq-bcl2fq-all-8xz6h                                                </span><br><span class="line"> └-·-● bcl2fq-bcl2fq-all-1  bcl2fq-bcl2fq-all-8xz6h-1539799166  10s       </span><br><span class="line">   ├-● bcl2fq-bcl2fq-all-2  bcl2fq-bcl2fq-all-8xz6h-1523021547  10s       </span><br><span class="line">   └-✔ bcl2fq-bcl2fq-all-3  bcl2fq-bcl2fq-all-8xz6h-1506243928  6s      </span><br></pre></td></tr></table></figure>
<p>我们可以看到有3个子pod被并行的执行了</p>
<figure class="highlight plain"><table><tr><td class="code"><pre><span class="line">Name:                bcl2fq-bcl2fq-all-8xz6h</span><br><span class="line">Namespace:           zanyuan</span><br><span class="line">ServiceAccount:      default</span><br><span class="line">Status:              Succeeded</span><br><span class="line">Created:             Thu Jul 11 18:14:13 +0800 (16 seconds ago)</span><br><span class="line">Started:             Thu Jul 11 18:14:13 +0800 (16 seconds ago)</span><br><span class="line">Finished:            Thu Jul 11 18:14:28 +0800 (1 second ago)</span><br><span class="line">Duration:            15 seconds</span><br><span class="line"></span><br><span class="line">STEP                        PODNAME                             DURATION  MESSAGE</span><br><span class="line"> ✔ bcl2fq-bcl2fq-all-8xz6h                                                </span><br><span class="line"> ├-·-✔ bcl2fq-bcl2fq-all-1  bcl2fq-bcl2fq-all-8xz6h-1539799166  8s        </span><br><span class="line"> | ├-✔ bcl2fq-bcl2fq-all-2  bcl2fq-bcl2fq-all-8xz6h-1523021547  9s        </span><br><span class="line"> | └-✔ bcl2fq-bcl2fq-all-3  bcl2fq-bcl2fq-all-8xz6h-1506243928  6s        </span><br><span class="line"> └---✔ sign                 bcl2fq-bcl2fq-all-8xz6h-2619111197  2s </span><br></pre></td></tr></table></figure>
<p>执行之后的目录结构如下：</p>
<figure class="highlight plain"><table><tr><td class="code"><pre><span class="line">.</span><br><span class="line">├── bcl2fq-all</span><br><span class="line">│   ├── bcl2fq-all_1.sh</span><br><span class="line">│   ├── bcl2fq-all_1.sh.e.bcl2fq-bcl2fq-all-khtpv-2956236467</span><br><span class="line">│   ├── bcl2fq-all_1.sh.o.bcl2fq-bcl2fq-all-khtpv-2956236467</span><br><span class="line">│   ├── bcl2fq-all_1.sh.sign</span><br><span class="line">│   ├── bcl2fq-all_2.sh</span><br><span class="line">│   ├── bcl2fq-all_2.sh.e.bcl2fq-bcl2fq-all-khtpv-2973014086</span><br><span class="line">│   ├── bcl2fq-all_2.sh.o.bcl2fq-bcl2fq-all-khtpv-2973014086</span><br><span class="line">│   ├── bcl2fq-all_2.sh.sign</span><br><span class="line">│   ├── bcl2fq-all_3.sh</span><br><span class="line">│   ├── bcl2fq-all_3.sh.e.bcl2fq-bcl2fq-all-khtpv-2989791705</span><br><span class="line">│   ├── bcl2fq-all_3.sh.o.bcl2fq-bcl2fq-all-khtpv-2989791705</span><br><span class="line">│   └── bcl2fq-all_3.sh.sign</span><br><span class="line">├── bcl2fq.ini</span><br><span class="line">├── bcl2fq.sh</span><br><span class="line">└── bcl2fq.sh.sign</span><br></pre></td></tr></table></figure>
<blockquote>
<p> 如果设置了lines，执行了投递操作</p>
</blockquote>
<ul>
<li> 会在<strong>container.args</strong>的value脚本所在目录建立一个目录，这个新建的目录以<strong>templetes.pod_name</strong>命名</li>
<li> <strong>container.args</strong>里的内容会按照lines的设置按行次序分割，并把分割后的内容输出到新建的目录里，命名为<strong>templetes.pod_name</strong>+<strong>_</strong>+<strong>分割的第几个单元(数字)</strong>+<strong>.sh</strong></li>
<li> <strong>标准输出流</strong>和<strong>标准错误</strong>会分别输出到对应子shell的<code>job_N.sh.o.+podID</code>、<code>job_N.sh.e.+podID</code>里</li>
<li> 每个子shell成功完成之后还会有一个<code>job_sh.sign</code>这个<code>job_sh.sign</code>里的内容为<code>**~/gomonitor.project.conf**</code>里<strong>base.defaultFinishMark</strong>对应value</li>
<li> 会伴随一个<code>container.args+.sign</code>的文件出现，文件里的内容为<code>**~/gomonitor.project.conf**</code>里<strong>base.defaultFinishMark</strong>对应value，示例如下：</li>
</ul>
<p><code>cat bcl2fq.ini.sign</code></p>
<p>Still_waters_run_deep</p>
<blockquote>
<p> 目前container.lines参数只对于<code>**-t**</code>选择为<code>argo</code>适用，对于<code>**-t**</code>选择为<code>pod</code>或者<code>job</code>无效</p>
</blockquote>
<h2 id="submit-a-pod-to-kubernetes" class="article-heading"><a href="#submit-a-pod-to-kubernetes" class="headerlink" title="submit a pod to kubernetes"></a>submit a pod to kubernetes<a class="article-anchor" href="#submit-a-pod-to-kubernetes" aria-hidden="true"></a></h2><p><code>cat k8sPodConf.ini</code></p>
<figure class="highlight shell"><table><tr><td class="code"><pre><span class="line">[templetes]</span><br><span class="line">pod_name = test</span><br><span class="line">imagePullSecrets = registry-read-only-key-yw</span><br><span class="line"></span><br><span class="line">[NodeSelector]</span><br><span class="line">env = idc_physical</span><br><span class="line"></span><br><span class="line">[requests]</span><br><span class="line">memory = 1</span><br><span class="line">cpu = 1</span><br><span class="line"></span><br><span class="line">[limits]</span><br><span class="line">memory = 1</span><br><span class="line">cpu = 1</span><br><span class="line"></span><br><span class="line">[container]</span><br><span class="line">image = registry-vpc.cn-hangzhou.aliyuncs.com/annoroad/annogene-base:v0.1</span><br><span class="line">args = /home/zanyuan/bin/example/taskmodeTest10/a1-base.sh</span><br><span class="line"></span><br><span class="line">[volumeMounts]</span><br><span class="line">home = /cluster_home|store|/home</span><br></pre></td></tr></table></figure>
<p><code>gomonitor submit -p k8sPodConf.ini -t pod</code></p>
<p>test-zxpm9</p>
<p><code>kubectl get pod test-zxpm9</code></p>
<figure class="highlight plain"><table><tr><td class="code"><pre><span class="line">NAME         READY     STATUS      RESTARTS   AGE</span><br><span class="line">test-zxpm9   0&#x2F;1       Completed   0          12s</span><br></pre></td></tr></table></figure>
<h2 id="submit-a-job-to-kubernetes" class="article-heading"><a href="#submit-a-job-to-kubernetes" class="headerlink" title="submit a job to kubernetes"></a>submit a job to kubernetes<a class="article-anchor" href="#submit-a-job-to-kubernetes" aria-hidden="true"></a></h2><p><code>gomonitor submit -p k8sPodConf.ini -t job</code></p>
<p>test-nxm9b</p>
<p><code>kubectl get job test-nxm9b</code></p>
<figure class="highlight plain"><table><tr><td class="code"><pre><span class="line">NAME         DESIRED   SUCCESSFUL   AGE</span><br><span class="line">test-nxm9b   1         1            11s</span><br></pre></td></tr></table></figure>
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